Tue, 23 Feb 2021

Package localScore updated to version 1.0.5 with previous version 1.0.4 dated 2021-02-23

Title: Package for Sequence Analysis by Local Score
Description: Functionalities for calculating the local score and calculating statistical relevance (p-value) to find a local Score in a sequence of given distribution (S. Mercier and J.-J. Daudin (2001) <https://hal.archives-ouvertes.fr/hal-00714174> ; S. Karlin and S. Altschul (1990) <https://www.pnas.org/content/87/6/2264> ; S. Mercier, D. Cellier and F. Charlot (2003) <https://hal.archives-ouvertes.fr/hal-00937529v1> ; A. Lagnoux, S. Mercier and P. Valois (2017) <doi:10.1093/bioinformatics/btw699> ).
Author: Sebastian Simon [aut], David Robelin [aut, cre], Sabine Mercier [aut], Sebastien Dejean [aut], The authors of Eigen the library for the included version of Eigen [cph]
Maintainer: David Robelin <david.robelin@inrae.fr>

Diff between localScore versions 1.0.4 dated 2021-02-23 and 1.0.5 dated 2021-02-23

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Package SEMsens updated to version 1.0.1 with previous version 0.2.6 dated 2020-07-18

Title: A Tool for Sensitivity Analysis in Structural Equation Modeling
Description: Perform sensitivity analysis in structural equation modeling using meta-heuristic optimization methods (e.g., ant colony optimization and others). The references for the proposed methods are: (1) Leite, W., & Shen, Z., Marcoulides, K., Fish, C., & Harring, J. (in press). Using ant colony optimization for sensitivity analysis in structural equation modeling. Structural Equation Modeling: A Multidisciplinary Journal. (2) Harring, J. R., McNeish, D. M., & Hancock, G. R. (2017) <doi:10.1080/10705511.2018.1506925>; (3) Socha, K., & Dorigo, M. (2008) <doi:10.1016/j.ejor.2006.06.046>. We also thank Dr. Krzysztof Socha for sharing his research on ant colony optimization algorithm with continuous domains and associated R code, which provided the base for the development of this package.
Author: Walter Leite [aut, cre], Zuchao Shen [aut], Gail Fish [ctb], YongSeok Lee [ctb], Sanaz Nazari [ctb], Jia Quan [ctb], Eric Wright [ctb], Huibin Zhang [ctb]
Maintainer: Walter Leite <walter.leite@coe.ufl.edu>

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Package saemix updated to version 2.4 with previous version 2.3 dated 2019-12-06

Title: Stochastic Approximation Expectation Maximization (SAEM) Algorithm
Description: The SAEMIX package implements the Stochastic Approximation EM algorithm for parameter estimation in (non)linear mixed effects models. The SAEM algorithm: - computes the maximum likelihood estimator of the population parameters, without any approximation of the model (linearisation, quadrature approximation,...), using the Stochastic Approximation Expectation Maximization (SAEM) algorithm, - provides standard errors for the maximum likelihood estimator - estimates the conditional modes, the conditional means and the conditional standard deviations of the individual parameters, using the Hastings-Metropolis algorithm. Several applications of SAEM in agronomy, animal breeding and PKPD analysis have been published by members of the Monolix group. Documentation about 'saemix' is provided by a comprehensive user guide in the inst folder, and a reference concerning the methods is the paper by Comets, Lavenu and Lavielle (2017, <doi:10.18637/jss.v080.i03>). See 'citation("saemix")' for details.
Author: Emmanuelle Comets [aut, cre] (<https://orcid.org/0000-0002-9150-9886>), Audrey Lavenu [ctb], Marc Lavielle [ctb], Maud Delattre [ctb]
Maintainer: Emmanuelle Comets <emmanuelle.comets@inserm.fr>

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Package RcmdrPlugin.UCA updated to version 4.3-3 with previous version 4.2-6 dated 2018-12-30

Title: UCA Rcmdr Plug-in
Description: Some extensions to Rcmdr (R Commander), randomness test, variance test for one normal sample and predictions using active model, made by R-UCA project and used in teaching statistics at University of Cadiz (UCA).
Author: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Maintainer: Manuel Munoz-Marquez <manuel.munoz@uca.es>

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Package CSTools updated to version 4.0.0 with previous version 3.1.0 dated 2020-07-02

Title: Assessing Skill of Climate Forecasts on Seasonal-to-Decadal Timescales
Description: Exploits dynamical seasonal forecasts in order to provide information relevant to stakeholders at the seasonal timescale. The package contains process-based methods for forecast calibration, bias correction, statistical and stochastic downscaling, optimal forecast combination and multivariate verification, as well as basic and advanced tools to obtain tailored products. This package was developed in the context of the ERA4CS project MEDSCOPE and the H2020 S2S4E project. Doblas-Reyes et al. (2005) <doi:10.1111/j.1600-0870.2005.00104.x>. Mishra et al. (2018) <doi:10.1007/s00382-018-4404-z>. Sanchez-Garcia et al. (2019) <doi:10.5194/asr-16-165-2019>. Straus et al. (2007) <doi:10.1175/JCLI4070.1>. Terzago et al. (2018) <doi:10.5194/nhess-18-2825-2018>. Torralba et al. (2017) <doi:10.1175/JAMC-D-16-0204.1>. D'Onofrio et al. (2014) <doi:10.1175/JHM-D-13-096.1>. Verfaillie et al. (2017) <doi:10.5194/gmd-10-4257-2017>. Van Schaeybroeck et al. (2019) <doi:10.1016/B978-0-12-812372-0.00010-8>. Yiou et al. (2013) <doi:10.1007/s00382-012-1626-3>.
Author: Nuria Perez-Zanon [aut, cre] (<https://orcid.org/0000-0001-8568-3071>), Louis-Philippe Caron [aut] (<https://orcid.org/0000-0001-5221-0147>), Carmen Alvarez-Castro [aut] (<https://orcid.org/0000-0002-9958-010X>), Lauriane Batte [aut], Jost von Hardenberg [aut] (<https://orcid.org/0000-0002-5312-8070>), Llorenç LLedo [aut], Nicolau Manubens [aut], Eroteida Sanchez-Garcia [aut], Bert van Schaeybroeck [aut], Veronica Torralba [aut], Deborah Verfaillie [aut], Filippo Cali Quaglia [ctb], Maria M. Chaves-Montero [ctb], Chihchung Chou [ctb], Nicola Cortesi [ctb], Susanna Corti [ctb], Paolo Davini [ctb], Gildas Dayon [ctb], Marta Dominguez [ctb], Federico Fabiano [ctb], Ignazio Giuntoli [ctb], Raul Marcos [ctb], Paola Marson [ctb], Niti Mishra [ctb], Jesus Peña [ctb], Francesc Roura-Adserias [ctb], Silvia Terzago [ctb], Danila Volpi [ctb], BSC-CNS [cph]
Maintainer: Nuria Perez-Zanon <nuria.perez@bsc.es>

Diff between CSTools versions 3.1.0 dated 2020-07-02 and 4.0.0 dated 2021-02-23

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Package prt updated to version 0.1.3 with previous version 0.1.2 dated 2020-09-29

Title: Tabular Data Backed by Partitioned 'fst' Files
Description: Intended for larger-than-memory tabular data, 'prt' objects provide an interface to read row and/or column subsets into memory as data.table objects. Data queries, constructed as 'R' expressions, are evaluated using the non-standard evaluation framework provided by 'rlang' and file-backing is powered by the fast and efficient 'fst' package.
Author: Nicolas Bennett [aut, cre], Drago Plecko [ctb]
Maintainer: Nicolas Bennett <nicolas.bennett@stat.math.ethz.ch>

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Package mvabund updated to version 4.1.9 with previous version 4.1.6 dated 2020-12-18

Title: Statistical Methods for Analysing Multivariate Abundance Data
Description: A set of tools for displaying, modeling and analysing multivariate abundance data in community ecology. See 'mvabund-package.Rd' for details of overall package organization. The package is implemented with the Gnu Scientific Library (<http://www.gnu.org/software/gsl/>) and 'Rcpp' (<http://dirk.eddelbuettel.com/code/rcpp.html>) 'R' / 'C++' classes.
Author: Yi Wang [aut], Ulrike Naumann [aut], Dirk Eddelbuettel [aut], John Wilshire [aut], David Warton [aut, cre], Julian Byrnes [ctb], Ralph dos Santos Silva [ctb, cph], Jenni Niku [ctb], Ian Renner [ctb], Stephen Wright [ctb]
Maintainer: David Warton <David.Warton@unsw.edu.au>

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Package rplos updated to version 1.0.0 with previous version 0.9.0 dated 2020-04-08

Title: Interface to the Search API for 'PLoS' Journals
Description: A programmatic interface to the 'SOLR' based search API (<http://api.plos.org/>) provided by the Public Library of Science journals to search their articles. Functions are included for searching for articles, retrieving articles, making plots, doing 'faceted' searches, 'highlight' searches, and viewing results of 'highlighted' searches in a browser.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>), Carl Boettiger [aut], Karthik Ram [aut], rOpenSci [fnd] (https://ropensci.org)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package ggmosaic updated to version 0.3.3 with previous version 0.2.0 dated 2018-09-12

Title: Mosaic Plots in the 'ggplot2' Framework
Description: Mosaic plots in the 'ggplot2' framework. Mosaic plot functionality is provided in a single 'ggplot2' layer by calling the geom 'mosaic'.
Author: Haley Jeppson [aut, cre], Heike Hofmann [aut], Di Cook [aut], Hadley Wickham [ctb]
Maintainer: Haley Jeppson <hjeppson@iastate.edu>

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Package eatGADS updated to version 0.16.0 with previous version 0.15.2 dated 2020-11-25

Title: Data Management of Large Hierarchical Data
Description: Import 'SPSS' data, handle and change 'SPSS' meta data, store and access large hierarchical data in 'SQLite' data bases.
Author: Benjamin Becker [aut, cre]
Maintainer: Benjamin Becker <b.becker@iqb.hu-berlin.de>

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Package tcR (with last version 2.3.2) was removed from CRAN

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2020-06-09 2.3.2
2020-03-22 2.2.4.1
2019-03-25 2.2.4
2019-01-07 2.2.3
2018-08-01 2.2.2
2016-04-22 2.2.1.11
2015-12-22 2.2.1.7
2015-11-07 2.2.1

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2018-11-03 1.1.0

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2020-04-21 1.2
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2014-05-30 0.1-18

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2016-02-24 1.55

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2020-12-08 1.0.0

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Package reproducer updated to version 0.4.2 with previous version 0.4.1 dated 2021-02-14

Title: Reproduce Statistical Analyses and Meta-Analyses
Description: Includes data analysis functions (e.g., to calculate effect sizes and 95% Confidence Intervals (CI) on Standardised Effect Sizes (d) for AB/BA cross-over repeated-measures experimental designs), data presentation functions (e.g., density curve overlaid on histogram), and the data sets analyzed in different research papers in software engineering (e.g., related to software defect prediction or multi-site experiment concerning the extent to which structured abstracts were clearer and more complete than conventional abstracts) to streamline reproducible research in software engineering.
Author: Lech Madeyski [cre, aut, ctb] (The main contributor and maintainer), Barbara Kitchenham [ctb] (Data and code contributor), Tomasz Lewowski [ctb] (Data and code contributor), Marian Jureczko [ctb] (Data contributor), David Budgen [ctb] (Data contributor), Pearl Brereton [ctb] (Data contributor), Jacky Keung [ctb] (Data contributor), Stuart Charters [ctb] (Data contributor), Shirley Gibbs [ctb] (Data contributor), Amnart Pohthong [ctb] (Data contributor), Giuseppe Scanniello [ctb] (Data contributor), Carmine Gravino [ctb] (Data contributor)
Maintainer: Lech Madeyski <lech.madeyski@gmail.com>

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Package DiceKriging updated to version 1.6.0 with previous version 1.5.8 dated 2020-11-05

Title: Kriging Methods for Computer Experiments
Description: Estimation, validation and prediction of kriging models. Important functions : km, print.km, plot.km, predict.km.
Author: Olivier Roustant, David Ginsbourger, Yves Deville. Contributors: Clement Chevalier, Yann Richet.
Maintainer: Olivier Roustant <roustant@insa-toulouse.fr>

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 man/leaveOneOut.km.Rd      |    7 +++++--
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More information about DiceKriging at CRAN
Permanent link

Package Boom updated to version 0.9.7 with previous version 0.9.6 dated 2020-04-30

Title: Bayesian Object Oriented Modeling
Description: A C++ library for Bayesian modeling, with an emphasis on Markov chain Monte Carlo. Although boom contains a few R utilities (mainly plotting functions), its primary purpose is to install the BOOM C++ library on your system so that other packages can link against it.
Author: Steven L. Scott is the sole author and creator of the BOOM project. Some code in the BOOM libraries has been modified from other open source projects. These include Cephes (obtained from Netlib, written by Stephen L. Moshier), NEWUOA (M.J.D Powell, obtained from Powell's web site), and a modified version of the R math libraries (R core development team). Original copyright notices have been maintained in all source files. In these cases, copyright claimed by Steven L. Scott is limited to modifications made to the original code. Google claims copyright for code written while Steven L. Scott was employed at Google from 2008 - 2018, but BOOM is not an officially supported Google project.
Maintainer: Steven L. Scott <steve.the.bayesian@gmail.com>

Diff between Boom versions 0.9.6 dated 2020-04-30 and 0.9.7 dated 2021-02-23

 DESCRIPTION                                                                 |    8 
 MD5                                                                         |  462 +++---
 inst/include/Bmath/Bmath.hpp                                                |    1 
 inst/include/Bmath/bessel.hpp                                               |only
 inst/include/Eigen/CMakeLists.txt                                           |only
 inst/include/Eigen/Cholesky                                                 |    5 
 inst/include/Eigen/Core                                                     |   34 
 inst/include/Eigen/Eigenvalues                                              |    8 
 inst/include/Eigen/Geometry                                                 |    4 
 inst/include/Eigen/LU                                                       |    4 
 inst/include/Eigen/QR                                                       |    8 
 inst/include/Eigen/QtAlignedMalloc                                          |    2 
 inst/include/Eigen/SVD                                                      |    4 
 inst/include/Eigen/SparseQR                                                 |    1 
 inst/include/Eigen/src/Cholesky/LDLT.h                                      |   14 
 inst/include/Eigen/src/Cholesky/LLT.h                                       |   26 
 inst/include/Eigen/src/Core/Array.h                                         |    2 
 inst/include/Eigen/src/Core/ArrayBase.h                                     |    4 
 inst/include/Eigen/src/Core/AssignEvaluator.h                               |   66 
 inst/include/Eigen/src/Core/Assign_MKL.h                                    |    6 
 inst/include/Eigen/src/Core/ConditionEstimator.h                            |    2 
 inst/include/Eigen/src/Core/CoreEvaluators.h                                |   39 
 inst/include/Eigen/src/Core/CwiseUnaryView.h                                |    2 
 inst/include/Eigen/src/Core/DenseBase.h                                     |    7 
 inst/include/Eigen/src/Core/DenseStorage.h                                  |    6 
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 inst/include/Eigen/src/Core/GeneralProduct.h                                |   21 
 inst/include/Eigen/src/Core/GenericPacketMath.h                             |    9 
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 inst/include/Eigen/src/Core/MathFunctionsImpl.h                             |   23 
 inst/include/Eigen/src/Core/Matrix.h                                        |    2 
 inst/include/Eigen/src/Core/MatrixBase.h                                    |   38 
 inst/include/Eigen/src/Core/PermutationMatrix.h                             |   28 
 inst/include/Eigen/src/Core/PlainObjectBase.h                               |   16 
 inst/include/Eigen/src/Core/Product.h                                       |   10 
 inst/include/Eigen/src/Core/ProductEvaluators.h                             |   59 
 inst/include/Eigen/src/Core/Redux.h                                         |    2 
 inst/include/Eigen/src/Core/Ref.h                                           |    7 
 inst/include/Eigen/src/Core/SelfAdjointView.h                               |    6 
 inst/include/Eigen/src/Core/SelfCwiseBinaryOp.h                             |    4 
 inst/include/Eigen/src/Core/SolveTriangular.h                               |    9 
 inst/include/Eigen/src/Core/StableNorm.h                                    |    2 
 inst/include/Eigen/src/Core/Transpose.h                                     |    2 
 inst/include/Eigen/src/Core/Transpositions.h                                |   41 
 inst/include/Eigen/src/Core/TriangularMatrix.h                              |    8 
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 inst/include/Eigen/src/Core/arch/AVX512/MathFunctions.h                     |   95 -
 inst/include/Eigen/src/Core/arch/AVX512/PacketMath.h                        |  729 ++++------
 inst/include/Eigen/src/Core/arch/AltiVec/Complex.h                          |   35 
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 inst/include/Eigen/src/Core/arch/CUDA/Half.h                                |  254 ++-
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 inst/include/Eigen/src/Core/arch/NEON/Complex.h                             |   12 
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 inst/include/Eigen/src/Core/arch/ZVector/Complex.h                          |    3 
 inst/include/Eigen/src/Core/functors/BinaryFunctors.h                       |   25 
 inst/include/Eigen/src/Core/functors/StlFunctors.h                          |    4 
 inst/include/Eigen/src/Core/functors/UnaryFunctors.h                        |    2 
 inst/include/Eigen/src/Core/products/GeneralBlockPanelKernel.h              |   22 
 inst/include/Eigen/src/Core/products/GeneralMatrixMatrix.h                  |   37 
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 inst/include/Eigen/src/Geometry/AngleAxis.h                                 |    2 
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 inst/include/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h           |    5 
 inst/include/Eigen/src/Jacobi/Jacobi.h                                      |  253 +--
 inst/include/Eigen/src/LU/InverseImpl.h                                     |    2 
 inst/include/Eigen/src/LU/PartialPivLU.h                                    |    5 
 inst/include/Eigen/src/LU/arch/Inverse_SSE.h                                |    4 
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 inst/include/Eigen/src/SVD/JacobiSVD_LAPACKE.h                              |    5 
 inst/include/Eigen/src/SVD/SVDBase.h                                        |    4 
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 inst/include/Eigen/src/SuperLUSupport/SuperLUSupport.h                      |    4 
 inst/include/Eigen/src/plugins/ArrayCwiseBinaryOps.h                        |    2 
 inst/include/LinAlg/Array.hpp                                               |   16 
 inst/include/LinAlg/Matrix.hpp                                              |   26 
 inst/include/LinAlg/SWEEP.hpp                                               |   15 
 inst/include/Models/CategoricalData.hpp                                     |   28 
 inst/include/Models/DataTypes.hpp                                           |   24 
 inst/include/Models/FiniteMixtureModel.hpp                                  |    5 
 inst/include/Models/Glm/GlmCoefs.hpp                                        |   12 
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 inst/include/Models/Glm/PosteriorSamplers/MultivariateRegressionSampler.hpp |    5 
 inst/include/Models/Glm/RegressionModel.hpp                                 |    6 
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 inst/include/Models/Glm/VariableSelectionPrior.hpp                          |    4 
 inst/include/Models/IRT/Item.hpp                                            |    9 
 inst/include/Models/IRT/PartialCreditModel.hpp                              |    4 
 inst/include/Models/Impute                                                  |only
 inst/include/Models/ModelTypes.hpp                                          |   18 
 inst/include/Models/MultinomialModel.hpp                                    |   27 
 inst/include/Models/ParamTypes.hpp                                          |   20 
 inst/include/Models/PointProcess/PoissonProcess.hpp                         |   14 
 inst/include/Models/PoissonModel.hpp                                        |    2 
 inst/include/Models/Policies/CompositeParamPolicy.hpp                       |    8 
 inst/include/Models/Policies/IID_DataPolicy.hpp                             |   17 
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 inst/include/Models/SpdParams.hpp                                           |    2 
 inst/include/Models/StateSpace/DynamicRegression.hpp                        |    8 
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 inst/include/Models/StateSpace/StateSpaceModelBase.hpp                      |    6 
 inst/include/Models/WishartModel.hpp                                        |    2 
 inst/include/TargetFun/Loglike.hpp                                          |    2 
 inst/include/cpputil/ParamHolder.hpp                                        |    9 
 inst/include/cpputil/ToString.hpp                                           |   13 
 inst/include/distributions.hpp                                              |   23 
 inst/include/distributions/Rmath_dist.hpp                                   |    2 
 inst/include/distributions/rng.hpp                                          |   14 
 inst/include/numopt/Integral.hpp                                            |   16 
 inst/include/r_interface/boom_r_tools.hpp                                   |   20 
 inst/include/stats/DataTable.hpp                                            |  289 +++
 inst/include/stats/ECDF.hpp                                                 |   16 
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 src/Bmath/Bmath.hpp                                                         |    1 
 src/Bmath/bessel.hpp                                                        |only
 src/Bmath/bessel_k.cpp                                                      |only
 src/LinAlg/Array.cpp                                                        |   74 -
 src/LinAlg/CorrelationMatrix.cpp                                            |    8 
 src/LinAlg/Matrix.cpp                                                       |  132 +
 src/LinAlg/SWEEP.cpp                                                        |   69 
 src/LinAlg/Vector.cpp                                                       |   28 
 src/LinAlg/VectorView.cpp                                                   |   17 
 src/Models/CategoricalData.cpp                                              |   29 
 src/Models/DataTypes.cpp                                                    |   28 
 src/Models/FiniteMixtureModel.cpp                                           |   21 
 src/Models/Glm/GlmCoefs.cpp                                                 |    5 
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 src/Models/Glm/MultivariateRegression.cpp                                   |   18 
 src/Models/Glm/MvtRegModel.cpp                                              |    6 
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 src/Models/Glm/PosteriorSamplers/MultivariateRegressionSampler.cpp          |   11 
 src/Models/Glm/RegressionModel.cpp                                          |    4 
 src/Models/Glm/TRegression.cpp                                              |    7 
 src/Models/Glm/VariableSelectionPrior.cpp                                   |   16 
 src/Models/IRT/DafePcrItemSampler.cpp                                       |    2 
 src/Models/IRT/PartialCreditModel.cpp                                       |    4 
 src/Models/Impute                                                           |only
 src/Models/Mixtures/PosteriorSamplers/SplitMerge.cpp                        |   43 
 src/Models/ModelTypes.cpp                                                   |    6 
 src/Models/MultinomialModel.cpp                                             |   55 
 src/Models/ParamTypes.cpp                                                   |    9 
 src/Models/PoissonModel.cpp                                                 |    2 
 src/Models/Policies/CompositeParamPolicy.cpp                                |    8 
 src/Models/Policies/NullParamPolicy.cpp                                     |   10 
 src/Models/PosteriorSamplers/MultinomialDirichletSampler.cpp                |   62 
 src/Models/SpdParams.cpp                                                    |    4 
 src/Models/StateSpace/PosteriorSamplers/DynamicRegressionDirectGibbs.cpp    |    4 
 src/Models/StateSpace/StateSpaceModelBase.cpp                               |    4 
 src/Models/TimeSeries/ArModel.cpp                                           |    1 
 src/Models/TimeSeries/PosteriorSamplers/NonzeroMeanAr1Sampler.cpp           |    6 
 src/Models/WishartModel.cpp                                                 |    2 
 src/boom_r_tools.cpp                                                        |   31 
 src/cpputil/ParamHolder.cpp                                                 |    6 
 src/distributions/Rmath_dist.cpp                                            |    4 
 src/distributions/gig.cpp                                                   |only
 src/distributions/mvn.cpp                                                   |   18 
 src/distributions/rng.cpp                                                   |   12 
 src/distributions/trun_gamma.cpp                                            |    6 
 src/stats/DataTable.cpp                                                     |  654 ++++++--
 src/stats/ECDF.cpp                                                          |   28 
 src/stats/Encoders.cpp                                                      |only
 src/stats/FreqDist.cpp                                                      |    4 
 src/stats/IQagent.cpp                                                       |   48 
 src/stats/hexbin.cpp                                                        |only
 src/stats/summary.cpp                                                       |  133 +
 238 files changed, 4459 insertions(+), 2578 deletions(-)

More information about Boom at CRAN
Permanent link

Package mlt.docreg updated to version 1.0-10 with previous version 1.0-9 dated 2020-12-15

Title: Most Likely Transformations: Documentation and Regression Tests
Description: Additional documentation, a package vignette and regression tests for package mlt.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

Diff between mlt.docreg versions 1.0-9 dated 2020-12-15 and 1.0-10 dated 2021-02-23

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More information about mlt.docreg at CRAN
Permanent link

Package episensr updated to version 1.0.0 with previous version 0.9.6 dated 2020-03-06

Title: Basic Sensitivity Analysis of Epidemiological Results
Description: Basic sensitivity analysis of the observed relative risks adjusting for unmeasured confounding and misclassification of the exposure/outcome, or both. It follows the bias analysis methods and examples from the book by Lash T.L, Fox M.P, and Fink A.K. "Applying Quantitative Bias Analysis to Epidemiologic Data", ('Springer', 2009).
Author: Denis Haine [aut, cre] (<https://orcid.org/0000-0002-6691-7335>)
Maintainer: Denis Haine <denis.haine@gmail.com>

Diff between episensr versions 0.9.6 dated 2020-03-06 and 1.0.0 dated 2021-02-23

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Package eirm updated to version 0.3 with previous version 0.2.0 dated 2020-10-27

Title: Explanatory Item Response Modeling for Dichotomous and Polytomous Items
Description: Analysis of dichotomous and polytomous response data using the explanatory item response modeling framework, as described in Stanke & Bulut (2019) <doi:10.21449/ijate.515085> and De Boeck & Wilson (2004) <doi:10.1007/978-1-4757-3990-9>. Generalized linear mixed modeling is used for estimating the effects of item-related and person-related variables on dichotomous and polytomous item responses.
Author: Okan Bulut [aut, cre] (<https://orcid.org/0000-0001-5853-1267>)
Maintainer: Okan Bulut <bulut@ualberta.ca>

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Package Dominance updated to version 1.2.0 with previous version 1.1.2 dated 2020-11-13

Title: Calculate and Visualize Dominance Hierarchies
Description: Functions to calculate ADI (Average Dominance Index) and FDI (Frequency-Based Dominance Index). Functions to visualize the Data with Social Network Graphs with Dual Directions and Music Notation Graph. 'XLConnect' or 'openxlsx' or 'RcmdrMisc' is only necessary for comfortable Excel file handling. See ADI-FDI Hemelrijk et al. (2005) <doi:10.1163/156853905774405290> de Vries et al. (2009) <doi:10.1163/156853909X412241> Musicnotition: Chase (2006) <doi:10.1186/1742-9994-3-18>.
Author: Knut Krueger [aut, cre], Konstanze Krueger [aut]
Maintainer: Knut Krueger <Knut.Krueger@equine-science.de>

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Package cli updated to version 2.3.1 with previous version 2.3.0 dated 2021-01-31

Title: Helpers for Developing Command Line Interfaces
Description: A suite of tools to build attractive command line interfaces ('CLIs'), from semantic elements: headings, lists, alerts, paragraphs, etc. Supports custom themes via a 'CSS'-like language. It also contains a number of lower level 'CLI' elements: rules, boxes, trees, and 'Unicode' symbols with 'ASCII' alternatives. It support ANSI colors and text styles as well.
Author: Gábor Csárdi [aut, cre], Hadley Wickham [ctb], Kirill Müller [ctb], RStudio [cph]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>

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Package JumpeR updated to version 0.1.3 with previous version 0.1.2 dated 2021-02-19

Title: Importing and Working with Track and Field Data
Description: Primarily used to convert human readable track and field results into dataframes for further analysis. Results can come from central repositories like <https://www.flashresults.com/> or <http://www.deltatiming.com/>, or from individual team sites, like those for colleges. Also contains functions useful for working with track and field data.
Author: Greg Pilgrim [aut, cre] (<https://orcid.org/0000-0001-7831-442X>), George Perry [ctb], Caitlin Baldwin [ctb]
Maintainer: Greg Pilgrim <gpilgrim2670@gmail.com>

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Package healthyR updated to version 0.1.2 with previous version 0.1.1 dated 2020-12-04

Title: Hospital Data Analysis Workflow Tools
Description: Hospital data analysis workflow tools, modeling, and automations. This library provides many useful tools to review common administrative hospital data. Some of these include average length of stay, readmission rates, average net pay amounts by service lines just to name a few. The aim is to provide a simple and consistent verb framework that takes the guesswork out of everything.
Author: Steven Sanderson [aut, cre], Steven Sanderson [cph]
Maintainer: Steven Sanderson <spsanderson@gmail.com>

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Package glmnetUtils updated to version 1.1.7 with previous version 1.1.6 dated 2020-10-06

Title: Utilities for 'Glmnet'
Description: Provides a formula interface for the 'glmnet' package for elasticnet regression, a method for cross-validating the alpha parameter, and other quality-of-life tools.
Author: Microsoft [cph], Hong Ooi [aut, cre]
Maintainer: Hong Ooi <hongooi73@gmail.com>

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Package CoOL updated to version 1.0.1 with previous version 1.0 dated 2021-02-12

Title: Causes of Outcome Learning
Description: Implementing the computational phase of the Causes of Outcome Learning approach as described in Rieckmann, Dworzynski, Arras, Lapuschkin, Samek, Arah, Rod, Ekstrom. Causes of outcome learning: A causal inference-inspired machine learning approach to disentangling common combinations of potential causes of a health outcome. medRxiv (2020) <doi:10.1101/2020.12.10.20225243>. The optional 'ggtree' package can be obtained through Bioconductor.
Author: Andreas Rieckmann [aut, cre], Piotr Dworzynski [aut], Leila Arras [ctb], Claus Thorn Ekstrom [aut]
Maintainer: Andreas Rieckmann <aric@sund.ku.dk>

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Package BAT updated to version 2.5.0 with previous version 2.4.2 dated 2021-01-22

Title: Biodiversity Assessment Tools
Description: Includes algorithms to assess alpha and beta diversity in all their dimensions (taxonomic, phylogenetic and functional). It allows performing a number of analyses based on species identities/abundances, phylogenetic/functional distances, trees, convex-hulls or kernel density n-dimensional hypervolumes depicting species relationships. Cardoso et al. (2015) <doi:10.1111/2041-210X.12310>.
Author: Pedro Cardoso [aut, cre], Stefano Mammola [aut], Francois Rigal [aut], Jose Carvalho [aut]
Maintainer: Pedro Cardoso <pedro.cardoso@helsinki.fi>

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Package TestDimorph updated to version 0.4.1 with previous version 0.4.0 dated 2021-01-10

Title: Analysis Of The Interpopulation Difference In Degree of Sexual Dimorphism Using Summary Statistics
Description: Offers a solution for the unavailability of raw data in most anthropological studies by facilitating the calculations of several sexual dimorphism related analyses using the published summary statistics of metric data (mean, standard deviation and sex specific sample size) as illustrated by the works of Greene, D. L. (1989) <doi:10.1002/ajpa.1330790113> and Konigsberg, L. W. (1991) <doi:10.1002/ajpa.1330840110>.
Author: Bassam A. Abulnoor [aut, cre] (<https://orcid.org/0000-0003-4351-2754>), MennattAllah H. Attia [aut] (<https://orcid.org/0000-0002-2304-532X>), Lyle W. Konigsberg [aut] (<https://orcid.org/0000-0003-4052-1575>)
Maintainer: Bassam A. Abulnoor <bassam.abulnoor@gmail.com>

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Package RFLPtools updated to version 1.8 with previous version 1.6 dated 2014-08-13

Title: Tools to Analyse RFLP Data
Description: Provides functions to analyse DNA fragment samples (i.e. derived from RFLP-analysis) and standalone BLAST report files (i.e. DNA sequence analysis).
Author: Fabienne Flessa [aut], Alexandra Kehl [aut] (<https://orcid.org/0000-0002-1547-0713>), Mohammed Aslam Imtiaz [aut], Matthias Kohl [aut, cre] (<https://orcid.org/0000-0001-9514-8910>)
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>

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Package psychonetrics updated to version 0.9 with previous version 0.8.1 dated 2021-01-28

Title: Structural Equation Modeling and Confirmatory Network Analysis
Description: Multi-group (dynamical) structural equation models in combination with confirmatory network models from cross-sectional, time-series and panel data <doi:10.31234/osf.io/8ha93>. Allows for confirmatory testing and fit as well as exploratory model search.
Author: Sacha Epskamp
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>

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Package pagoda2 updated to version 1.0.1 with previous version 1.0.0 dated 2021-01-28

Title: Single Cell Analysis and Differential Expression
Description: Analyzing and interactively exploring large-scale single-cell RNA-seq datasets. 'pagoda2' primarily performs normalization and differential gene expression analysis, with an interactive application for exploring single-cell RNA-seq datasets. It performs basic tasks such as cell size normalization, gene variance normalization, and can be used to identify subpopulations and run differential expression within individual samples. 'pagoda2' was written to rapidly process modern large-scale scRNAseq datasets of approximately 1e6 cells. The companion web application allows users to explore which gene expression patterns form the different subpopulations within your data. The package also serves as the primary method for preprocessing data for conos, <https://github.com/kharchenkolab/conos>. This package interacts with data available through the 'p2data' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/pagoda2>. The size of the 'p2data' package is approximately 6 MB.
Author: Nikolas Barkas [aut], Viktor Petukhov [aut], Peter Kharchenko [aut], Simon Steiger [ctb], Evan Biederstedt [cre, aut]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>

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Package MXM updated to version 1.5.1 with previous version 1.5.0 dated 2021-01-08

Title: Feature Selection (Including Multiple Solutions) and Bayesian Networks
Description: Many feature selection methods for a wide range of response variables, including minimal, statistically-equivalent and equally-predictive feature subsets. Bayesian network algorithms and related functions are also included. The package name 'MXM' stands for "Mens eX Machina", meaning "Mind from the Machine" in Latin. References: a) Lagani, V. and Athineou, G. and Farcomeni, A. and Tsagris, M. and Tsamardinos, I. (2017). Feature Selection with the R Package MXM: Discovering Statistically Equivalent Feature Subsets. Journal of Statistical Software, 80(7). <doi:10.18637/jss.v080.i07>. b) Tsagris, M., Lagani, V. and Tsamardinos, I. (2018). Feature selection for high-dimensional temporal data. BMC Bioinformatics, 19:17. <doi:10.1186/s12859-018-2023-7>. c) Tsagris, M., Borboudakis, G., Lagani, V. and Tsamardinos, I. (2018). Constraint-based causal discovery with mixed data. International Journal of Data Science and Analytics, 6(1): 19-30. <doi:10.1007/s41060-018-0097-y>. d) Tsagris, M., Papadovasilakis, Z., Lakiotaki, K. and Tsamardinos, I. (2018). Efficient feature selection on gene expression data: Which algorithm to use? BioRxiv. <doi:10.1101/431734>. e) Tsagris, M. (2019). Bayesian Network Learning with the PC Algorithm: An Improved and Correct Variation. Applied Artificial Intelligence, 33(2):101-123. <doi:10.1080/08839514.2018.1526760>. f) Tsagris, M. and Tsamardinos, I. (2019). Feature selection with the R package MXM. F1000Research 7: 1505. <doi:10.12688/f1000research.16216.2>. g) Borboudakis, G. and Tsamardinos, I. (2019). Forward-Backward Selection with Early Dropping. Journal of Machine Learning Research 20: 1-39. h) The gamma-OMP algorithm for feature selection with application to gene expression data. IEEE/ACM Transactions on Computational Biology and Bioinformatics (Accepted for publication) <doi:10.1109/TCBB.2020.3029952>.
Author: Michail Tsagris [aut, cre], Ioannis Tsamardinos [aut, cph], Vincenzo Lagani [aut, cph], Giorgos Athineou [aut], Giorgos Borboudakis [ctb], Anna Roumpelaki [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>

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Package kokudosuuchi updated to version 1.0.0 with previous version 0.4.2 dated 2018-01-25

Title: Utilities for 'Kokudo Suuchi'
Description: Provides utilities for 'Kokudo Suuchi', the GIS data service of the Japanese government. See <https://nlftp.mlit.go.jp/index.html> for more information.
Author: Hiroaki Yutani [aut, cre] (<https://orcid.org/0000-0002-3385-7233>)
Maintainer: Hiroaki Yutani <yutani.ini@gmail.com>

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New package ergMargins with initial version 0.1.2
Package: ergMargins
Type: Package
Title: Process Analysis for Exponential Random Graph Models
Version: 0.1.2
Authors@R: person("Scott", "Duxbury",email="duxbury@email.unc.edu", role=c("aut", "cre", "cph"))
Maintainer: Scott Duxbury <duxbury@email.unc.edu>
Description: Calculates marginal effects and conducts process analysis in exponential family random graph models (ERGM). Includes functions to conduct mediation and moderation analyses and to diagnose multicollinearity. URL: <https://github.com/sduxbury/ergMargins>. BugReports: <https://github.com/sduxbury/ergMargins/issues>. Duxbury, Scott W (2021) <doi:10.1177/0049124120986178>. Long, J. Scott, and Sarah Mustillo (2018) <doi:10.1177/0049124118799374>. Mize, Trenton D. (2019) <doi:10.15195/v6.a4>. Karlson, Kristian Bernt, Anders Holm, and Richard Breen (2012) <doi:10.1177/0081175012444861>. Duxbury, Scott W (2018) <doi:10.1177/0049124118782543>.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Imports: numDeriv, statnet, stats, ergm, Matrix, network, btergm, methods, sna, xergm.common
Suggests: MASS, knitr, rmarkdown
NeedsCompilation: no
Packaged: 2021-02-23 13:31:37 UTC; sduxb
Author: Scott Duxbury [aut, cre, cph]
Repository: CRAN
Date/Publication: 2021-02-23 14:50:05 UTC

More information about ergMargins at CRAN
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Package CoxICPen updated to version 1.1.0 with previous version 1.0.0 dated 2021-02-17

Title: Variable Selection for Cox's Model with Interval-Censored Data
Description: Perform variable selection for Cox regression model with interval-censored data. Can deal with both low-dimensional and high-dimensional data. Case-cohort design can be incorporated. Two sets of covariates scenario can also be considered. The references are listed in the URL below.
Author: Qiwei Wu [aut, cre], Hui Zhao [aut], Jianguo Sun [aut]
Maintainer: Qiwei Wu <qw235@mail.missouri.edu>

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Package nmaINLA updated to version 1.0.0 with previous version 0.2.0 dated 2020-04-07

Title: Network Meta-Analysis using Integrated Nested Laplace Approximations
Description: Performs network meta-analysis using integrated nested Laplace approximations ('INLA') which is described in Guenhan, Held, and Friede (2018) <doi:10.1002/jrsm.1285>. Includes methods to assess the heterogeneity and inconsistency in the network. Contains more than ten different network meta-analysis dataset. 'INLA' package can be obtained from <https://www.r-inla.org>.
Author: Burak Kuersad Guenhan [aut, cre] (<https://orcid.org/0000-0002-7454-8680>)
Maintainer: Burak Kuersad Guenhan <burak.gunhan@med.uni-goettingen.de>

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Package sccore updated to version 0.1.2 with previous version 0.1.1 dated 2020-12-14

Title: Core Utilities for Single-Cell RNA-Seq
Description: Core utilities for single-cell RNA-seq data analysis. Contained within are utility functions for working with differential expression (DE) matrices and count matrices, a collection of functions for manipulating and plotting data via 'ggplot2', and functions to work with cell graphs and cell embeddings. Graph-based methods include embedding kNN cell graphs into a UMAP <doi:10.21105/joss.00861>, collapsing vertices of each cluster in the graph, and propagating graph labels.
Author: Viktor Petukhov [aut], Ramus Rydbirk [aut], Peter Kharchenko [aut], Evan Biederstedt [aut, cre]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>

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Package Rdpack updated to version 2.1.1 with previous version 2.1 dated 2020-11-09

Title: Update and Manipulate Rd Documentation Objects
Description: Functions for manipulation of R documentation objects, including functions reprompt() and ereprompt() for updating 'Rd' documentation for functions, methods and classes; 'Rd' macros for citations and import of references from 'bibtex' files for use in 'Rd' files and 'roxygen2' comments; 'Rd' macros for evaluating and inserting snippets of 'R' code and the results of its evaluation or creating graphics on the fly; and many functions for manipulation of references and Rd files.
Author: Georgi N. Boshnakov [aut, cre], Duncan Murdoch [ctb]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>

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Package pkgload updated to version 1.2.0 with previous version 1.1.0 dated 2020-05-29

Title: Simulate Package Installation and Attach
Description: Simulates the process of installing a package and then attaching it. This is a key part of the 'devtools' package as it allows you to rapidly iterate while developing a package.
Author: Hadley Wickham [aut], Jim Hester [aut, cre], Winston Chang [aut], RStudio [cph], R Core team [ctb] (Some namespace and vignette code extracted from base R)
Maintainer: Jim Hester <jim.hester@rstudio.com>

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Package partitions updated to version 1.10-2 with previous version 1.10-1 dated 2021-02-12

Title: Additive Partitions of Integers
Description: Additive partitions of integers. Enumerates the partitions, unequal partitions, and restricted partitions of an integer; the three corresponding partition functions are also given. Set partitions and now compositions are included.
Author: Robin K. S. Hankin [aut, cre] (<https://orcid.org/0000-0001-5982-0415>), Paul Egeler [ctb] (<https://orcid.org/0000-0001-6948-9498>)
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>

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Package loon updated to version 1.3.2 with previous version 1.3.1 dated 2020-06-17

Title: Interactive Statistical Data Visualization
Description: An extendable toolkit for interactive data visualization and exploration.
Author: Adrian Waddell [aut], R. Wayne Oldford [aut, cre, ths], Zehao Xu [ctb], Martin Gauch [ctb]
Maintainer: R. Wayne Oldford <rwoldford@uwaterloo.ca>

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Package imager updated to version 0.42.7 with previous version 0.42.3 dated 2020-05-11

Title: Image Processing Library Based on 'CImg'
Description: Fast image processing for images in up to 4 dimensions (two spatial dimensions, one time/depth dimension, one colour dimension). Provides most traditional image processing tools (filtering, morphology, transformations, etc.) as well as various functions for easily analysing image data using R. The package wraps 'CImg', <http://cimg.eu>, a simple, modern C++ library for image processing.
Author: Simon Barthelme [aut], David Tschumperle [ctb], Jan Wijffels [ctb], Haz Edine Assemlal [ctb], Shota Ochi [cre]
Maintainer: Shota Ochi <shotaochi1990@gmail.com>

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Package gtrendsR updated to version 1.4.8 with previous version 1.4.7 dated 2020-09-12

Title: Perform and Display Google Trends Queries
Description: An interface for retrieving and displaying the information returned online by Google Trends is provided. Trends (number of hits) over the time as well as geographic representation of the results can be displayed.
Author: Philippe Massicotte [aut, cre], Dirk Eddelbuettel [aut]
Maintainer: Philippe Massicotte <pmassicotte@hotmail.com>

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Package ggsignif updated to version 0.6.1 with previous version 0.6.0 dated 2019-08-08

Title: Significance Brackets for 'ggplot2'
Description: Enrich your 'ggplots' with group-wise comparisons. This package provides an easy way to indicate if two groups are significantly different. Commonly this is shown by a bracket on top connecting the groups of interest which itself is annotated with the level of significance (NS, *, **, ***). The package provides a single layer (geom_signif()) that takes the groups for comparison and the test (t.test(), wilcox.text() etc.) as arguments and adds the annotation to the plot.
Author: Constantin Ahlmann-Eltze [aut, cre, ctb] (<https://orcid.org/0000-0002-3762-068X>, @const_ae), Indrajeet Patil [aut, ctb] (<https://orcid.org/0000-0003-1995-6531>, @patilindrajeets)
Maintainer: Constantin Ahlmann-Eltze <artjom31415@googlemail.com>

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Package ggraph updated to version 2.0.5 with previous version 2.0.4 dated 2020-11-16

Title: An Implementation of Grammar of Graphics for Graphs and Networks
Description: The grammar of graphics as implemented in ggplot2 is a poor fit for graph and network visualizations due to its reliance on tabular data input. ggraph is an extension of the ggplot2 API tailored to graph visualizations and provides the same flexible approach to building up plots layer by layer.
Author: Thomas Lin Pedersen [cre, aut] (<https://orcid.org/0000-0002-5147-4711>), RStudio [cph]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>

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Package eefAnalytics updated to version 1.0.10 with previous version 1.0.8 dated 2020-10-22

Title: Robust Analytical Methods for Evaluating Educational Interventions using Randomised Controlled Trials Designs
Description: Analysing data from evaluations of educational interventions using a randomised controlled trial design. Various analytical tools to perform sensitivity analysis using different methods are supported (e.g. frequentist models with bootstrapping and permutations options, Bayesian models). The included commands can be used for simple randomised trials, cluster randomised trials and multisite trials. The methods can also be used more widely beyond education trials. This package can be used to evaluate other intervention designs using Frequentist and Bayesian multilevel models.
Author: Germaine Uwimpuhwe, Akansha Singh, Steve Higgins, ZhiMin Xiao, Ewoud De Troyer and Adetayo Kasim
Maintainer: Germaine Uwimpuhwe <germaine.uwimpuhwe@durham.ac.uk>

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Package dyngen updated to version 1.0.0 with previous version 0.4.0 dated 2020-09-10

Title: A Multi-Modal Simulator for Spearheading Single-Cell Omics Analyses
Description: A novel, multi-modal simulation engine for studying dynamic cellular processes at single-cell resolution. 'dyngen' is more flexible than current single-cell simulation engines. It allows better method development and benchmarking, thereby stimulating development and testing of novel computational methods. Cannoodt et al. (2020) <doi:10.1101/2020.02.06.936971>.
Author: Robrecht Cannoodt [aut, cre, cph] (<https://orcid.org/0000-0003-3641-729X>), Wouter Saelens [aut] (<https://orcid.org/0000-0002-7114-6248>)
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>

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Package datamods updated to version 1.1.0 with previous version 1.0.1 dated 2021-02-16

Title: Modules to Import and Manipulate Data in 'Shiny'
Description: 'Shiny' modules to import data into an application or 'addin' from various sources, and to manipulate them after that.
Author: Victor Perrier [aut, cre, cph], Fanny Meyer [aut], Zauad Shahreer Abeer [aut]
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>

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Package cwbtools updated to version 0.3.3 with previous version 0.3.2 dated 2021-02-17

Title: Tools to Create, Modify and Manage 'CWB' Corpora
Description: The 'Corpus Workbench' ('CWB', <http://cwb.sourceforge.net/>) offers a classic and mature approach for working with large, linguistically and structurally annotated corpora. The 'CWB' is memory efficient and its design makes running queries fast (Evert and Hardie 2011, <http://www.stefan-evert.de/PUB/EvertHardie2011.pdf>). The 'cwbtools' package offers pure R tools to create indexed corpus files as well as high-level wrappers for the original C implementation of CWB as exposed by the 'RcppCWB' package <https://CRAN.R-project.org/package=RcppCWB>. Additional functionality to add and modify annotations of corpora from within R makes working with CWB indexed corpora much more flexible and convenient. The 'cwbtools' package in combination with the R packages 'RcppCWB' (<https://CRAN.R-project.org/package=RcppCWB>) and 'polmineR' (<https://CRAN.R-project.org/package=polmineR>) offers a lightweight infrastructure to support the combination of quantitative and qualitative approaches for working with textual data.
Author: Andreas Blaette [aut, cre], Christoph Leonhardt [ctb]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>

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Package CausalImpact updated to version 1.2.6 with previous version 1.2.5 dated 2021-01-04

Title: Inferring Causal Effects using Bayesian Structural Time-Series Models
Description: Implements a Bayesian approach to causal impact estimation in time series, as described in Brodersen et al. (2015) <DOI:10.1214/14-AOAS788>. See the package documentation on GitHub <https://google.github.io/CausalImpact/> to get started.
Author: Kay H. Brodersen <kbrodersen@google.com>, Alain Hauser <alhauser@google.com>
Maintainer: Alain Hauser <alhauser@google.com>

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Package multibridge updated to version 1.1.0 with previous version 1.0.0 dated 2021-01-25

Title: Evaluating Multinomial Order Restrictions with Bridge Sampling
Description: Evaluate hypotheses concerning the distribution of multinomial proportions using bridge sampling. The bridge sampling routine is able to compute Bayes factors for hypotheses that entail inequality constraints, equality constraints, free parameters, and mixtures of all three. These hypotheses are tested against the encompassing hypothesis, that all parameters vary freely or against the null hypothesis that all category proportions are equal. For more information see Sarafoglou et al. (2020) <doi:10.31234/osf.io/bux7p>.
Author: Alexandra Sarafoglou [aut, cre] (<https://orcid.org/0000-0003-0031-685X>), Frederik Aust [aut] (<https://orcid.org/0000-0003-4900-788X>), Julia M. Haaf [aut] (<https://orcid.org/0000-0001-5122-706X>), Joris Goosen [aut], Quentin F. Gronau [aut], Maarten Marsman [aut] (<https://orcid.org/0000-0001-5309-7502>)
Maintainer: Alexandra Sarafoglou <alexandra.sarafoglou@gmail.com>

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Package sparkxgb updated to version 0.1.1 with previous version 0.1.0 dated 2019-03-13

Title: Interface for 'XGBoost' on 'Apache Spark'
Description: A 'sparklyr' <https://spark.rstudio.com/> extension that provides an R interface for 'XGBoost' <https://github.com/dmlc/xgboost> on 'Apache Spark'. 'XGBoost' is an optimized distributed gradient boosting library.
Author: Kevin Kuo [aut] (<https://orcid.org/0000-0001-7803-7901>), Yitao Li [aut, cre] (<https://orcid.org/0000-0002-1261-905X>)
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Package rSPDE updated to version 0.6.2 with previous version 0.4.8 dated 2020-03-08

Title: Rational Approximations of Fractional Stochastic Partial Differential Equations
Description: Functions that compute rational approximations of fractional elliptic stochastic partial differential equations. The package also contains functions for common statistical usage of these approximations. The main reference for the methods is Bolin and Kirchner (2020) <doi:10.1080/10618600.2019.1665537>, which can be generated by the citation function in R.
Author: David Bolin [cre, aut]
Maintainer: David Bolin <davidbolin@gmail.com>

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Package ralger updated to version 2.2.3 with previous version 2.2.2 dated 2021-02-18

Title: Easy Web Scraping
Description: The goal of 'ralger' is to facilitate web scraping in R.
Author: Mohamed El Fodil Ihaddaden [aut, cre], Ezekiel Ogundepo [ctb], Romain François [ctb]
Maintainer: Mohamed El Fodil Ihaddaden <ihaddaden.fodeil@gmail.com>

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Package oxcAAR updated to version 1.1.0 with previous version 1.0.0 dated 2018-02-09

Title: Interface to 'OxCal' Radiocarbon Calibration
Description: A set of tools that enables using 'OxCal' from within R. 'OxCal' (<https://c14.arch.ox.ac.uk/oxcal.html>) is a standard archaeological tool intended to provide 14C calibration and analysis of archaeological and environmental chronological information. 'OxcAAR' allows simple calibration with 'Oxcal' and plotting of the results as well as the execution of sophisticated ('OxCal') code and the import of the results of bulk analysis and complex Bayesian sequential calibration.
Author: Hinz Martin [aut, cre], Clemens Schmid [aut], Daniel Knitter [aut], Carolin Tietze [aut]
Maintainer: Hinz Martin <martin.hinz@iaw.unibe.ch>

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Package leaflegend updated to version 0.2.0 with previous version 0.1.0 dated 2021-01-25

Title: Add Custom Legends to 'leaflet' Maps
Description: Provides extensions to the 'leaflet' package to customize legends with images, text styling, orientation, sizing, and symbology.
Author: Thomas Roh [aut, cre]
Maintainer: Thomas Roh <thomas@roh.engineering>

Diff between leaflegend versions 0.1.0 dated 2021-01-25 and 0.2.0 dated 2021-02-23

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More information about leaflegend at CRAN
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Package spacefillr updated to version 0.2.0 with previous version 0.1.0 dated 2021-02-17

Title: Space-Filling Random and Quasi-Random Sequences
Description: Generates random and quasi-random space-filling sequences. Supports the following sequences: 'Halton', 'Sobol', 'Owen'-scrambled 'Sobol', 'Owen'-scrambled 'Sobol' with errors distributed as blue noise, progressive jittered, progressive multi-jittered ('PMJ'), 'PMJ' with blue noise, 'PMJ02', and 'PMJ02' with blue noise. Includes a 'C++' 'API'. Methods derived from "Constructing Sobol sequences with better two-dimensional projections" (2012) <doi:10.1137/070709359> S. Joe and F. Y. Kuo, "Progressive Multi-Jittered Sample Sequences" (2018) <https://graphics.pixar.com/library/ProgressiveMultiJitteredSampling/paper.pdf> Christensen, P., Kensler, A. and Kilpatrick, C., and "A Low-Discrepancy Sampler that Distributes Monte Carlo Errors as a Blue Noise in Screen Space" (2019) E. Heitz, B. Laurent, O. Victor, C. David and I. Jean-Claude, <doi:10.1145/3306307.3328191>.
Author: Tyler Morgan-Wall [aut, cph, cre] (<https://orcid.org/0000-0002-3131-3814>), Andrew Helmer [ctb, cph], Leonhard Grünschloß [ctb, cph], Eric Heitz [ctb, cph]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>

Diff between spacefillr versions 0.1.0 dated 2021-02-17 and 0.2.0 dated 2021-02-23

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Package rsubgroup updated to version 1.1 with previous version 1.0 dated 2020-04-22

Title: Subgroup Discovery and Analytics
Description: A collection of efficient and effective tools and algorithms for subgroup discovery and analytics. The package integrates an R interface to the org.vikamine.kernel library of the VIKAMINE system <http://www.vikamine.org> implementing subgroup discovery, pattern mining and analytics in Java.
Author: Martin Atzmueller
Maintainer: Martin Atzmueller <martin@atzmueller.net>

Diff between rsubgroup versions 1.0 dated 2020-04-22 and 1.1 dated 2021-02-23

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New package regioncode with initial version 0.1.0
Package: regioncode
Title: Convert Region Names and Division Codes of China Over Years
Version: 0.1.0
Authors@R: c(person(given = "Yue",family = "Hu",role = c("aut","cre"), email = "yuehu@tsinghua.edu.cn"), person(given = "Yufei",family = "Sun",role = c("aut"), email = "sunyf20@mails.tsinghua.edu.cn"), person(given = "Wenquan",family = "Wu",role = c("aut"), email = "gohuntsuan@gmail.com"), person(given = "Yuyang",family = "Shi",role = c("ctb"), email = "yangtzesyy@gmail.com"), person(given = "Yujia",family = "Xu",role = c("ctb"), email = "593878126@qq.com"), person(given = "Yuxin",family = "Pan",role = c("ctb"), email = "panyx17@mails.tsinghua.edu.cn"), person(given = "Haiting",family = "Tian",role = c("ctb"), email = "tianht.18@sem.tsingha.edu.cn"), person(given = "Weihang",family = "Shao",role = c("ctb"), email = "shaowh19@mails.tsinghua.edu.cn"), person(given = "Yuanqian",family = "Chen",role = c("ctb"), email = "yuanqian18@mails.tsinghua.edu.cn"))
Author: Yue Hu [aut, cre], Yufei Sun [aut], Wenquan Wu [aut], Yuyang Shi [ctb], Yujia Xu [ctb], Yuxin Pan [ctb], Haiting Tian [ctb], Weihang Shao [ctb], Yuanqian Chen [ctb]
Maintainer: Yue Hu <yuehu@tsinghua.edu.cn>
Description: A fast tool to conquer the difficulties to convert various region names and administration division codes of Chinese regions. The current version enables seamlessly converting Chinese regions' formal names, common-used names, and codes between each other at the city level from 1986 to 2019.
License: MIT + file LICENSE
Encoding: UTF-8
BugReports: https://github.com/sammo3182/regioncode/issues
Depends: R(>= 3.6.0)
Imports: dplyr, knitr, textshaping
Suggests: rmarkdown
LazyData: true
RoxygenNote: 7.1.1
Config/testthat/edition: 3
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-02-23 06:36:21 UTC; sunyufei
Repository: CRAN
Date/Publication: 2021-02-23 09:50:02 UTC

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Package PheVis updated to version 1.0.2 with previous version 1.0.1 dated 2021-02-16

Title: Automatic Phenotyping of Electronic Health Record at Visit Resolution
Description: Using Electronic Health Record (EHR) is difficult because most of the time the true characteristic of the patient is not available. Instead we can retrieve the International Classification of Disease code related to the disease of interest or we can count the occurrence of the Unified Medical Language System. None of them is the true phenotype which needs chart review to identify. However chart review is time consuming and costly. 'PheVis' is an algorithm which is phenotyping (i.e identify a characteristic) at the visit level in an unsupervised fashion. It can be used for chronic or acute diseases. An example of how to use 'PheVis' is available in the vignette. Basically there are two functions that are to be used: `train_phevis()` which trains the algorithm and `test_phevis()` which get the predicted probabilities. The detailed method is described in preprint by Ferté et al. (2020) <doi:10.1101/2020.06.15.20131458>.
Author: Thomas Ferte [aut, cre], Boris P. Hejblum [aut]
Maintainer: Thomas Ferte <thomas.ferte@u-bordeaux.fr>

Diff between PheVis versions 1.0.1 dated 2021-02-16 and 1.0.2 dated 2021-02-23

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More information about PheVis at CRAN
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Package midasr updated to version 0.8 with previous version 0.7 dated 2019-03-05

Title: Mixed Data Sampling Regression
Description: Methods and tools for mixed frequency time series data analysis. Allows estimation, model selection and forecasting for MIDAS regressions.
Author: Virmantas Kvedaras <virmantas.kvedaras@ec.europa.eu>, Vaidotas Zemlys-Balevicius <zemlys@gmail.com>
Maintainer: Vaidotas Zemlys-Balevičius <zemlys@gmail.com>

Diff between midasr versions 0.7 dated 2019-03-05 and 0.8 dated 2021-02-23

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Package metapack updated to version 0.1.1 with previous version 0.1.0 dated 2021-02-17

Title: Bayesian Meta-Analysis and Network Meta-Analysis
Description: Contains functions performing Bayesian inference for meta-analytic and network meta-analytic models through Markov chain Monte Carlo algorithm. Currently, the package implements Yao, Kim, Chen, Ibrahim, Shah, and Jianxin Lin (2015) <doi:10.1080/01621459.2015.1006065> and network meta-regression models using heavy-tailed multivariate random effects with covariate-dependent variances. For maximal computational efficiency, the Markov chain Monte Carlo samplers for each model, written in C++, are fine-tuned. This software has been developed under the auspices of the National Institutes of Health and Merck & Co., Inc., Kenilworth, NJ, USA.
Author: Daeyoung Lim [aut, cre], Ming-Hui Chen [ctb], Sungduk Kim [ctb], Joseph Ibrahim [ctb], Arvind Shah [ctb], Jianxin Lin [ctb]
Maintainer: Daeyoung Lim <daeyoung.lim@uconn.edu>

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Package lefko3 updated to version 3.3.1 with previous version 3.2.0 dated 2021-01-06

Title: Historical and Ahistorical Population Projection Matrix Analysis
Description: Creates matrix population models for use in population ecological analyses. Specializes on the construction of historical matrices, which are 2d matrices comprising 3 consecutive times of demographic information. Estimates both raw and function-based forms of historical and standard ahistorical matrices. It also estimates function-based age-by-stage matrices. Methodology based on Ehrlen (2000) <doi:10.1890/0012-9658(2000)081[1675:TDOPPD]2.0.CO;2>.
Author: Richard P. Shefferson [aut, cre] (<https://orcid.org/0000-0002-5234-3131>), Johan Ehrlen [aut] (<https://orcid.org/0000-0001-8539-8967>)
Maintainer: Richard P. Shefferson <cdorm@g.ecc.u-tokyo.ac.jp>

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New package gatepoints with initial version 0.1.4
Package: gatepoints
Title: Easily Gate or Select Points on a Scatter Plot
Version: 0.1.4
Authors@R: person("Wajid", "Jawaid", email = "wj241@alumni.cam.ac.uk", role = c("aut", "cre"))
Description: Allows user to choose/gate a region on the plot and returns points within it.
Depends: R (>= 3.0.0)
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
URL: https://github.com/wjawaid/gatepoints
NeedsCompilation: no
Packaged: 2021-02-13 23:35:18 UTC; wajid
Author: Wajid Jawaid [aut, cre]
Maintainer: Wajid Jawaid <wj241@alumni.cam.ac.uk>
Repository: CRAN
Date/Publication: 2021-02-23 09:40:13 UTC

More information about gatepoints at CRAN
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Package BayesMallows updated to version 1.0.1 with previous version 1.0.0 dated 2021-01-08

Title: Bayesian Preference Learning with the Mallows Rank Model
Description: An implementation of the Bayesian version of the Mallows rank model (Vitelli et al., Journal of Machine Learning Research, 2018 <https://jmlr.org/papers/v18/15-481.html>; Crispino et al., Annals of Applied Statistics, 2019 <doi:10.1214/18-AOAS1203>). Both Cayley, footrule, Hamming, Kendall, Spearman, and Ulam distances are supported in the models. The rank data to be analyzed can be in the form of complete rankings, top-k rankings, partially missing rankings, as well as consistent and inconsistent pairwise preferences. Several functions for plotting and studying the posterior distributions of parameters are provided. The package also provides functions for estimating the partition function (normalizing constant) of the Mallows rank model, both with the importance sampling algorithm of Vitelli et al. and asymptotic approximation with the IPFP algorithm (Mukherjee, Annals of Statistics, 2016 <doi:10.1214/15-AOS1389>).
Author: Oystein Sorensen [aut, cre] (<https://orcid.org/0000-0003-0724-3542>), Valeria Vitelli [aut] (<https://orcid.org/0000-0002-6746-0453>), Marta Crispino [aut], Qinghua Liu [aut], Cristina Mollica [aut], Luca Tardella [aut]
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>

Diff between BayesMallows versions 1.0.0 dated 2021-01-08 and 1.0.1 dated 2021-02-23

 DESCRIPTION                                         |    6 
 MD5                                                 |  236 ++---
 NAMESPACE                                           |   58 -
 NEWS.md                                             |  266 +++---
 R/BayesMallows.R                                    |   64 -
 R/Lik_DB_MIX.R                                      |  137 +--
 R/RcppExports.R                                     |  386 ++++-----
 R/assess_convergence.R                              |  396 ++++-----
 R/assign_cluster.R                                  |  164 +--
 R/compute_consensus.R                               |  414 ++++-----
 R/compute_mallows.R                                 |  848 ++++++++++----------
 R/compute_mallows_mixtures.R                        |   90 +-
 R/compute_posterior_intervals.R                     |  256 +++---
 R/data.R                                            |   62 -
 R/estimate_partition_function.R                     |  214 ++---
 R/expected_dist.R                                   |  100 +-
 R/generate_constraints.R                            |  162 +--
 R/generate_initial_ranking.R                        |  116 +-
 R/generate_transitive_closure.R                     |  214 ++---
 R/label_switching.R                                 |   42 
 R/misc.R                                            |  144 +--
 R/misc_expected_dist.R                              |  222 ++---
 R/misc_likelihood.R                                 |  142 +--
 R/obs_freq.R                                        |   24 
 R/plot.BayesMallows.R                               |  282 +++---
 R/plot_elbow.R                                      |  134 +--
 R/plot_top_k.R                                      |  168 +--
 R/predict_top_k.R                                   |  126 +-
 R/print.BayesMallows.R                              |   52 -
 R/print.BayesMallowsMixtures.R                      |   58 -
 R/rank_conversion.R                                 |  178 ++--
 R/rank_distance.R                                   |   80 -
 R/rank_freq_distr.R                                 |   56 -
 R/sample_mallows.R                                  |  284 +++---
 R/tidy_mcmc.R                                       |  506 +++++------
 build/partial.rdb                                   |binary
 build/vignette.rds                                  |binary
 inst/CITATION                                       |   30 
 inst/REFERENCES.bib                                 |  564 ++++++-------
 inst/doc/BayesMallows.pdf.asis                      |    4 
 inst/examples/Lik_DB_MIX_example.R                  |   95 +-
 inst/examples/compute_consensus_example.R           |  128 +--
 inst/examples/compute_mallows_example.R             |  240 ++---
 inst/examples/compute_mallows_mixtures_example.R    |  122 +-
 inst/examples/compute_posterior_intervals_example.R |   56 -
 inst/examples/estimate_partition_function_example.R |  130 +--
 inst/examples/expected_dist_example.R               |   12 
 inst/examples/generate_constraints_example.R        |   42 
 inst/examples/generate_initial_ranking_example.R    |   78 -
 inst/examples/generate_transitive_closure_example.R |  106 +-
 inst/examples/label_switching_example.R             |  150 +--
 inst/examples/obs_freq_example.R                    |  230 ++---
 inst/examples/plot.BayesMallows_example.R           |   98 +-
 inst/examples/plot_top_k_example.R                  |   42 
 inst/examples/rank_distance_example.R               |   30 
 inst/examples/rank_freq_distr_example.R             |   12 
 inst/examples/sample_mallows_example.R              |   98 +-
 man/BayesMallows.Rd                                 |   66 -
 man/assess_convergence.Rd                           |   76 -
 man/assign_cluster.Rd                               |   90 +-
 man/asymptotic_partition_function.Rd                |   82 -
 man/beach_preferences.Rd                            |   38 
 man/compute_consensus.Rd                            |  214 ++---
 man/compute_importance_sampling_estimate.Rd         |   56 -
 man/compute_mallows.Rd                              |  726 ++++++++---------
 man/compute_mallows_mixtures.Rd                     |  180 ++--
 man/compute_posterior_intervals.Rd                  |  154 +--
 man/dot-generate_transitive_closure.Rd              |   32 
 man/estimate_partition_function.Rd                  |  270 +++---
 man/expected_dist.Rd                                |   58 -
 man/generate_constraints.Rd                         |  112 +-
 man/generate_initial_ranking.Rd                     |  144 +--
 man/generate_transitive_closure.Rd                  |  204 ++--
 man/get_partition_function.Rd                       |   76 -
 man/get_rank_distance.Rd                            |   68 -
 man/label_switching.Rd                              |  198 ++--
 man/lik_db_mix.Rd                                   |  189 ++--
 man/log_expected_dist.Rd                            |   50 -
 man/obs_freq.Rd                                     |  260 +++---
 man/plot.BayesMallows.Rd                            |  162 +--
 man/plot_elbow.Rd                                   |  188 ++--
 man/plot_top_k.Rd                                   |  116 +-
 man/potato_true_ranking.Rd                          |   38 
 man/potato_visual.Rd                                |   42 
 man/potato_weighing.Rd                              |   42 
 man/predict_top_k.Rd                                |   64 -
 man/print.BayesMallows.Rd                           |   34 
 man/print.BayesMallowsMixtures.Rd                   |   34 
 man/rank_conversion.Rd                              |  120 +-
 man/rank_distance.Rd                                |  106 +-
 man/rank_freq_distr.Rd                              |   60 -
 man/rmallows.Rd                                     |   94 +-
 man/run_mcmc.Rd                                     |  218 ++---
 man/sample_mallows.Rd                               |  238 ++---
 man/sushi_rankings.Rd                               |   40 
 man/validate_permutation.Rd                         |   36 
 tests/testthat.R                                    |   10 
 tests/testthat/test-Lik_DB_MIX.R                    |  122 +-
 tests/testthat/test-rank_freq_distr.R               |  122 +-
 tests/testthat/test_assess_convergence.R            |   28 
 tests/testthat/test_compute_consensus.R             |  362 ++++----
 tests/testthat/test_compute_mallows.R               |  352 ++++----
 tests/testthat/test_distance_function.R             |  224 ++---
 tests/testthat/test_estimate_partition_function.R   |   88 +-
 tests/testthat/test_expected_dist.R                 |   30 
 tests/testthat/test_generate_ranking.R              |   50 -
 tests/testthat/test_mcmc_function.R                 |   80 -
 tests/testthat/test_misc_cpp.R                      |  102 +-
 tests/testthat/test_misc_functions.R                |   46 -
 tests/testthat/test_partition_function.R            |  242 ++---
 tests/testthat/test_plot.R                          |   20 
 tests/testthat/test_plot_elbow.R                    |   24 
 tests/testthat/test_plot_top_k.R                    |  164 +--
 tests/testthat/test_print.R                         |   40 
 tests/testthat/test_random_number_seed.R            |  100 +-
 tests/testthat/test_rank_conversion.R               |   52 -
 tests/testthat/test_sample_mallows.R                |   68 -
 tests/testthat/test_transitive_closure.R            |  100 +-
 vignettes/BayesMallows.pdf.asis                     |    4 
 119 files changed, 8195 insertions(+), 8164 deletions(-)

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New package arcpullr with initial version 0.1.2
Package: arcpullr
Type: Package
Title: Pull Data from an 'ArcGIS REST' API
Version: 0.1.2
Authors@R: c(person(given = "Paul", family = "Frater", role = c("aut", "cre"), email = "paul.frater@wisconsin.gov", comment = c(ORCID = "0000-0002-7237-6563")), person("Zac", "Driscoll", email = "zdriscoll@mmsd.com", role = c("aut"), comment = c(ORCID = "0000-0002-8233-0980")))
License: GPL-3
Encoding: UTF-8
LazyData: true
Description: Functions to efficiently query 'ArcGIS REST' APIs <https://developers.arcgis.com/rest/>. Both spatial and SQL queries can be used to retrieve data. Simple Feature (sf) objects are utilized to perform spatial queries. This package was neither produced nor is maintained by Esri.
Depends: R (>= 3.6.0)
Imports: httr (>= 1.4.1), jsonlite (>= 1.6.1), dplyr (>= 1.0.2), ggplot2 (>= 3.3.0), sf (>= 0.9.7), tidyr (>= 1.0.2), rlang (>= 0.4.7)
RoxygenNote: 7.1.1
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-02-19 03:03:12 UTC; fratepnd
Author: Paul Frater [aut, cre] (<https://orcid.org/0000-0002-7237-6563>), Zac Driscoll [aut] (<https://orcid.org/0000-0002-8233-0980>)
Maintainer: Paul Frater <paul.frater@wisconsin.gov>
Repository: CRAN
Date/Publication: 2021-02-23 09:40:16 UTC

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New package ammistability with initial version 0.1.2
Package: ammistability
Type: Package
Title: Additive Main Effects and Multiplicative Interaction Model Stability Parameters
Version: 0.1.2
Authors@R: c(person(given = c("B.", "C."), family = "Ajay", role = c("aut", "cre"), email = "ajaygpb@yahoo.co.in", comment = c(ORCID = "0000-0001-7222-8483")), person(given = "J.", family = "Aravind", role = "aut", email = "j.aravind@icar.gov.in", comment = c(ORCID = "0000-0002-4791-442X")), person(given = "R.", family = "Abdul Fiyaz", role = "aut", email = "fiyaz.ra@icar.gov.in", comment = c(ORCID = "0000-0001-6261-7071")), person(given = "ICAR", role = "cph", comment = c(url = "https://www.icar.org.in")))
Description: Computes various stability parameters from Additive Main Effects and Multiplicative Interaction (AMMI) analysis results such as Modified AMMI Stability Value (MASV), Sums of the Absolute Value of the Interaction Principal Component Scores (SIPC), Sum Across Environments of Genotype-Environment Interaction Modelled by AMMI (AMGE), Sum Across Environments of Absolute Value of Genotype-Environment Interaction Modelled by AMMI (AV_(AMGE)), AMMI Stability Index (ASI), Modified ASI (MASI), AMMI Based Stability Parameter (ASTAB), Annicchiarico's D Parameter (DA), Zhang's D Parameter (DZ), Averages of the Squared Eigenvector Values (EV), Stability Measure Based on Fitted AMMI Model (FA), Absolute Value of the Relative Contribution of IPCs to the Interaction (Za). Further calculates the Simultaneous Selection Index for Yield and Stability from the computed stability parameters. See the vignette for complete list of citations for the methods implemented.
Copyright: 2017-2020, ICAR-DGR
License: GPL-2 | GPL-3
Encoding: UTF-8
Depends: R (>= 3.5.0)
VignetteBuilder: knitr
RoxygenNote: 7.1.1
Imports: agricolae, ggcorrplot, ggplot2, methods, reshape2, stats, Rdpack, mathjaxr
Suggests: knitr, rmarkdown, pander, XML, httr, RCurl
RdMacros: Rdpack, mathjaxr
URL: https://github.com/ajaygpb/ammistability/ https://CRAN.R-project.org/package=ammistability https://ajaygpb.github.io/ammistability/ https://doi.org/10.5281/zenodo.1344756
BugReports: https://github.com/ajaygpb/ammistability/issues
NeedsCompilation: no
Packaged: 2021-02-21 21:24:07 UTC; J. Aravind
Author: B. C. Ajay [aut, cre] (<https://orcid.org/0000-0001-7222-8483>), J. Aravind [aut] (<https://orcid.org/0000-0002-4791-442X>), R. Abdul Fiyaz [aut] (<https://orcid.org/0000-0001-6261-7071>), ICAR [cph] (https://www.icar.org.in)
Maintainer: B. C. Ajay <ajaygpb@yahoo.co.in>
Repository: CRAN
Date/Publication: 2021-02-23 09:40:19 UTC

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New package terrainr with initial version 0.3.1
Package: terrainr
Type: Package
Title: Landscape Visualizations in R and 'Unity'
Version: 0.3.1
Authors@R: c( person(given = "Michael", family = "Mahoney", role = c("aut", "cre"), email = "mike.mahoney.218@gmail.com", comment = c(ORCID = "0000-0003-2402-304X")), person(given = "Mike", family = "Johnson", role = c("rev"), comment = c("Mike reviewed the package (v. 0.2.1) for rOpenSci, see <https://github.com/ropensci/software-review/issues/416>")), person(given = "Sydney", family = "Foks", role = c("rev"), comment = c("Sydney reviewed the package (v. 0.2.1) for rOpenSci, see <https://github.com/ropensci/software-review/issues/416>")))
Description: Functions for the retrieval, manipulation, and visualization of 'geospatial' data, with an aim towards producing '3D' landscape visualizations in the 'Unity' '3D' rendering engine. Functions are also provided for retrieving elevation data and base map tiles from the 'USGS' National Map ('<https://apps.nationalmap.gov/services/>').
URL: https://docs.ropensci.org/terrainr/, https://github.com/ropensci/terrainr
BugReports: https://github.com/ropensci/terrainr/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: base64enc, httr, raster, magick (>= 2.5.0), gdalUtils, methods, png, sf, units, grDevices, ggplot2
RoxygenNote: 7.1.1
Suggests: testthat, covr, progressr, knitr, rmarkdown, progress, jpeg, tiff, brio
Config/testthat/parallel: true
Config/testthat/edition: 3
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-02-22 16:46:14 UTC; mikemahoney218
Author: Michael Mahoney [aut, cre] (<https://orcid.org/0000-0003-2402-304X>), Mike Johnson [rev] (Mike reviewed the package (v. 0.2.1) for rOpenSci, see <https://github.com/ropensci/software-review/issues/416>), Sydney Foks [rev] (Sydney reviewed the package (v. 0.2.1) for rOpenSci, see <https://github.com/ropensci/software-review/issues/416>)
Maintainer: Michael Mahoney <mike.mahoney.218@gmail.com>
Repository: CRAN
Date/Publication: 2021-02-23 08:30:02 UTC

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New package localScore with initial version 1.0.4
Package: localScore
Type: Package
Title: Package for Sequence Analysis by Local Score
Version: 1.0.4
Date: 2021-02-22
Authors@R: c(person("Sebastian", "Simon", role = "aut"), person("David", "Robelin", role = c("aut","cre"), email = "david.robelin@inrae.fr"), person("Sabine", "Mercier", role = "aut", email = "sabine.mercier@univ-tlse2.fr"), person("Sebastien", "Dejean", role = "aut", email="sebastien.dejean@math.univ-toulouse.fr"), person(given="The authors of Eigen the library for the included version of Eigen", role = "cph"))
Copyright: See the file COPYRIGHTS for various embedded Eigen library copyright details
Maintainer: David Robelin <david.robelin@inrae.fr>
Description: Functionalities for calculating the local score and calculating statistical relevance (p-value) to find a local Score in a sequence of given distribution (S. Mercier and J.-J. Daudin (2001) <https://hal.archives-ouvertes.fr/hal-00714174> ; S. Karlin and S. Altschul (1990) <https://www.pnas.org/content/87/6/2264> ; S. Mercier, D. Cellier and F. Charlot (2003) <https://hal.archives-ouvertes.fr/hal-00937529v1> ; A. Lagnoux, S. Mercier and P. Valois (2017) <doi:10.1093/bioinformatics/btw699> ).
License: GPL (>= 2) | file LICENSE
Imports: Rcpp (>= 0.12.16), utils
LinkingTo: Rcpp
RoxygenNote: 7.1.1
LazyData: true
Encoding: UTF-8
SystemRequirements: C++11
Suggests: knitr, rmarkdown, testthat (>= 2.1.0)
VignetteBuilder: knitr
Depends: R (>= 3.2.0)
NeedsCompilation: yes
Packaged: 2021-02-22 16:39:34 UTC; drobelin
Author: Sebastian Simon [aut], David Robelin [aut, cre], Sabine Mercier [aut], Sebastien Dejean [aut], The authors of Eigen the library for the included version of Eigen [cph]
Repository: CRAN
Date/Publication: 2021-02-23 08:50:03 UTC

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New package gtfstools with initial version 0.1.0
Type: Package
Package: gtfstools
Title: General Transit Feed Specification (GTFS) Editing and Analysing Tools
Version: 0.1.0
Authors@R: c(person(given = "Daniel", family = "Herszenhut", role = c("aut", "cre"), email = "dhersz@gmail.com", comment = c(ORCID = "0000-0001-8066-1105")), person(given = "Ipea - Institute for Applied Economic Research", role = c("cph", "fnd")))
Description: Utility functions to read, manipulate, analyse and write transit feeds in the General Transit Feed Specification (GTFS) data format.
License: MIT + file LICENSE
URL: https://ipeagit.github.io/gtfstools/, https://github.com/ipeaGIT/gtfstools
BugReports: https://github.com/ipeaGIT/gtfstools/issues
Depends: R (>= 2.10)
Imports: checkmate, data.table, methods, sf, sfheaders, units, utils, zip
Suggests: covr, knitr, lwgeom, rmarkdown, testthat
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2021-02-22 18:03:48 UTC; dhersz
Author: Daniel Herszenhut [aut, cre] (<https://orcid.org/0000-0001-8066-1105>), Ipea - Institute for Applied Economic Research [cph, fnd]
Maintainer: Daniel Herszenhut <dhersz@gmail.com>
Repository: CRAN
Date/Publication: 2021-02-23 09:00:02 UTC

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New package conos with initial version 1.4.0
Package: conos
Title: Clustering on Network of Samples
Version: 1.4.0
Authors@R: c(person("Viktor","Petukhov", email="viktor.s.petuhov@ya.ru", role="aut"), person("Nikolas","Barkas", email="nikolas_barkas@hms.harvard.edu", role="aut"), person("Peter", "Kharchenko", email = "peter_kharchenko@hms.harvard.edu", role = "aut"), person("Weiliang", "Qiu", email = "weiliang.qiu@gmail.com", role = c("ctb")), person("Evan", "Biederstedt", email="evan.biederstedt@gmail.com", role=c("aut", "cre")))
Description: Wires together large collections of single-cell RNA-seq datasets, which allows for both the identification of recurrent cell clusters and the propagation of information between datasets in multi-sample or atlas-scale collections. 'Conos' focuses on the uniform mapping of homologous cell types across heterogeneous sample collections. For instance, users could investigate a collection of dozens of peripheral blood samples from cancer patients combined with dozens of controls, which perhaps includes samples of a related tissue such as lymph nodes. This package interacts with data available through the 'conosPanel' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/conos>. The size of the 'conosPanel' package is approximately 12 MB.
License: GPL-3
Copyright: See the file COPYRIGHTS for various conos copyright details
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0), Matrix, igraph
biocViews:
Imports: abind, cowplot, ComplexHeatmap, dendextend, dplyr, ggplot2, ggrepel, gridExtra, irlba, leidenAlg, magrittr, Matrix.utils, methods, N2R, parallel, R6, reshape2, rlang, Rtsne, sccore (>= 0.1.1), stats, tools, utils
RoxygenNote: 7.1.1
Suggests: AnnotationDbi, BiocParallel, conosPanel, DESeq2, entropy, ggrastr, GO.db, jsonlite, knitr, org.Hs.eg.db, org.Mm.eg.db, p2data, pagoda2, pbapply, PMA, pROC, plyr, rhdf5, rmarkdown, rmumps, Seurat, shinycssloaders, SummarizedExperiment, testthat, tibble, uwot, zoo
Additional_repositories: https://kharchenkolab.github.io/drat/
URL: https://github.com/kharchenkolab/conos
BugReports: https://github.com/kharchenkolab/conos/issues
NeedsCompilation: yes
LinkingTo: Rcpp, RcppArmadillo, RcppEigen, RcppProgress
Author: Viktor Petukhov [aut], Nikolas Barkas [aut], Peter Kharchenko [aut], Weiliang Qiu [ctb], Evan Biederstedt [aut, cre]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>
Packaged: 2021-02-22 20:38:30 UTC; evanbiederstedt
Repository: CRAN
Date/Publication: 2021-02-23 09:00:06 UTC

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Package shinyjqui updated to version 0.4.0 with previous version 0.3.3 dated 2020-02-03

Title: 'jQuery UI' Interactions and Effects for Shiny
Description: An extension to shiny that brings interactions and animation effects from 'jQuery UI' library.
Author: Yang Tang [aut, cre]
Maintainer: Yang Tang <tang_yang@outlook.com>

Diff between shinyjqui versions 0.3.3 dated 2020-02-03 and 0.4.0 dated 2021-02-23

 shinyjqui-0.3.3/shinyjqui/R/includeJqueryUI.R                                         |only
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 shinyjqui-0.4.0/shinyjqui/DESCRIPTION                                                 |   11 
 shinyjqui-0.4.0/shinyjqui/MD5                                                         |  110 +-
 shinyjqui-0.4.0/shinyjqui/NAMESPACE                                                   |   10 
 shinyjqui-0.4.0/shinyjqui/NEWS.md                                                     |   23 
 shinyjqui-0.4.0/shinyjqui/R/bookmarking.R                                             |only
 shinyjqui-0.4.0/shinyjqui/R/effects.R                                                 |  122 --
 shinyjqui-0.4.0/shinyjqui/R/icon.R                                                    |    2 
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 shinyjqui-0.4.0/shinyjqui/R/sortableTableOutput.R                                     |    2 
 shinyjqui-0.4.0/shinyjqui/R/utils.R                                                   |  143 +++
 shinyjqui-0.4.0/shinyjqui/README.md                                                   |   66 +
 shinyjqui-0.4.0/shinyjqui/build/vignette.rds                                          |binary
 shinyjqui-0.4.0/shinyjqui/inst/doc/introduction.R                                     |  145 +--
 shinyjqui-0.4.0/shinyjqui/inst/doc/introduction.Rmd                                   |  257 +++---
 shinyjqui-0.4.0/shinyjqui/inst/doc/introduction.html                                  |  424 +++++-----
 shinyjqui-0.4.0/shinyjqui/inst/doc/orderInput.R                                       |   27 
 shinyjqui-0.4.0/shinyjqui/inst/doc/orderInput.Rmd                                     |   46 -
 shinyjqui-0.4.0/shinyjqui/inst/doc/orderInput.html                                    |  131 ++-
 shinyjqui-0.4.0/shinyjqui/inst/doc/save-and-restore.R                                 |   39 
 shinyjqui-0.4.0/shinyjqui/inst/doc/save-and-restore.Rmd                               |   51 +
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 shinyjqui-0.4.0/shinyjqui/inst/shinydemos/orderInput_bookmarking.R                    |    8 
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 shinyjqui-0.4.0/shinyjqui/inst/shinydemos/resizable_combine_with_other_interactions.R |    6 
 shinyjqui-0.4.0/shinyjqui/inst/shinydemos/sortable_bookmarking.R                      |    2 
 shinyjqui-0.4.0/shinyjqui/inst/shinydemos/sortable_save_load.R                        |    2 
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More information about shinyjqui at CRAN
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Package Rmpi updated to version 0.6-9.1 with previous version 0.6-9 dated 2018-11-13

Title: Interface (Wrapper) to MPI (Message-Passing Interface)
Description: An interface (wrapper) to MPI. It also provides interactive R manager and worker environment.
Author: Hao Yu [aut]
Maintainer: Hao Yu <hyu@stats.uwo.ca>

Diff between Rmpi versions 0.6-9 dated 2018-11-13 and 0.6-9.1 dated 2021-02-23

 DESCRIPTION                    |   10 ++---
 MD5                            |   70 ++++++++++++++++++++---------------------
 R/Rmpi.R                       |   38 +++++++++++-----------
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Package BOJ updated to version 0.2.3 with previous version 0.2.2 dated 2020-05-25

Title: Interface to Bank of Japan Statistics
Description: Provides an interface to data provided by the Bank of Japan <https://www.boj.or.jp>.
Author: Stefan Angrick [aut, cre, cph]
Maintainer: Stefan Angrick <contact@stefanangrick.net>

Diff between BOJ versions 0.2.2 dated 2020-05-25 and 0.2.3 dated 2021-02-23

 DESCRIPTION        |   10 +-
 LICENSE            |    2 
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 build/vignette.rds |binary
 inst/doc/BOJ.R     |   24 +++--
 inst/doc/BOJ.Rmd   |   28 +++---
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 vignettes/BOJ.Rmd  |   28 +++---
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Package covid19nytimes (with last version 0.1.3) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2020-05-08 0.1.3

Permanent link
Package covid19mobility (with last version 0.1.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2020-07-20 0.1.1

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Package upstartr updated to version 0.1.1 with previous version 0.1.0 dated 2021-02-15

Title: Utilities Powering the Globe and Mail's Data Journalism Template
Description: Core functions necessary for using The Globe and Mail's R data journalism template, 'startr', along with utilities for day-to-day data journalism tasks, such as reading and writing files, producing graphics and cleaning up datasets.
Author: Tom Cardoso [aut, cre] (creator and maintainer), Michael Pereira [ctb], The Globe and Mail Inc. [cph]
Maintainer: Tom Cardoso <tcardoso@globeandmail.com>

Diff between upstartr versions 0.1.0 dated 2021-02-15 and 0.1.1 dated 2021-02-23

 DESCRIPTION       |    6 +++---
 MD5               |   10 +++++-----
 NEWS.md           |    7 +++++++
 R/init.R          |    2 +-
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 man/write_plot.Rd |    5 ++++-
 6 files changed, 25 insertions(+), 17 deletions(-)

More information about upstartr at CRAN
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